From c03a35ae9b9419c1df0f69f38a33000a3daaa3a8 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Mon, 18 Feb 2019 16:28:40 +0100
Subject: [PATCH] state docs
---
docs/state/readme.md | 6 ++++++
docs/state/transforms.md | 38 +++++++++++++++++++++++++++++++++-----
2 files changed, 39 insertions(+), 5 deletions(-)
diff --git a/docs/state/readme.md b/docs/state/readme.md
index bc20ea3df..22ae1ccc6 100644
--- a/docs/state/readme.md
+++ b/docs/state/readme.md
@@ -8,6 +8,8 @@ interface Snapshot {
data?: State.Snapshot,
// Snapshot of behavior state tree
behaviour?: State.Snapshot,
+ // Snapshot for current animation,
+ animation?: PluginAnimationManager.Snapshot,
// Saved camera positions
cameraSnapshots?: CameraSnapshotManager.StateSnapshot,
canvas3d?: {
@@ -69,6 +71,10 @@ interface Transform.Props {
"Built-in" data state transforms and description of their parameters are defined in ``mol-plugin/state/transforms``. Behavior transforms are defined in ``mol-plugin/behavior``. Auto-generated documentation for the transforms is also [available](transforms.md).
+# Animation State
+
+Defined by ``CameraSnapshotManager.StateSnapshot`` in ``mol-plugin/state/animation/manager.ts``.
+
# Canvas3D State
Defined by ``Canvas3DParams`` in ``mol-canvas3d/canvas3d.ts``.
diff --git a/docs/state/transforms.md b/docs/state/transforms.md
index f02e38b68..473030fad 100644
--- a/docs/state/transforms.md
+++ b/docs/state/transforms.md
@@ -7,9 +7,11 @@
* [ms-plugin.parse-ccp4](#ms-plugin-parse-ccp4)
* [ms-plugin.parse-dsn6](#ms-plugin-parse-dsn6)
* [ms-plugin.trajectory-from-mmcif](#ms-plugin-trajectory-from-mmcif)
+* [ms-plugin.trajectory-from-pdb](#ms-plugin-trajectory-from-pdb)
* [ms-plugin.model-from-trajectory](#ms-plugin-model-from-trajectory)
* [ms-plugin.structure-from-model](#ms-plugin-structure-from-model)
* [ms-plugin.structure-assembly-from-model](#ms-plugin-structure-assembly-from-model)
+* [ms-plugin.structure-symmetry-from-model](#ms-plugin-structure-symmetry-from-model)
* [ms-plugin.structure-selection](#ms-plugin-structure-selection)
* [ms-plugin.structure-complex-element](#ms-plugin-structure-complex-element)
* [ms-plugin.custom-model-properties](#ms-plugin-custom-model-properties)
@@ -65,7 +67,7 @@
----------------------------
## <a name="ms-plugin-parse-ccp4"></a>ms-plugin.parse-ccp4 :: Binary -> Ccp4
-*Parse CCP4/MRC from Binary data*
+*Parse CCP4/MRC/MAP from Binary data*
----------------------------
## <a name="ms-plugin-parse-dsn6"></a>ms-plugin.parse-dsn6 :: Binary -> Dsn6
@@ -82,6 +84,9 @@
```js
{}
```
+----------------------------
+## <a name="ms-plugin-trajectory-from-pdb"></a>ms-plugin.trajectory-from-pdb :: String -> Trajectory
+
----------------------------
## <a name="ms-plugin-model-from-trajectory"></a>ms-plugin.model-from-trajectory :: Trajectory -> Model
*Create a molecular structure from the specified model.*
@@ -104,13 +109,36 @@
*Create a molecular structure assembly.*
### Parameters
-- **id**?: String *(Assembly Id. If none specified (undefined or empty string), the asymmetric unit is used.)*
+- **id**?: String *(Assembly Id. Value 'deposited' can be used to specify deposited asymmetric unit.)*
### Default Parameters
```js
{}
```
----------------------------
+## <a name="ms-plugin-structure-symmetry-from-model"></a>ms-plugin.structure-symmetry-from-model :: Model -> Structure
+*Create a molecular structure symmetry.*
+
+### Parameters
+- **ijkMin**: 3D vector [x, y, z]
+- **ijkMax**: 3D vector [x, y, z]
+
+### Default Parameters
+```js
+{
+ "ijkMin": [
+ -1,
+ -1,
+ -1
+ ],
+ "ijkMax": [
+ 1,
+ 1,
+ 1
+ ]
+}
+```
+----------------------------
## <a name="ms-plugin-structure-selection"></a>ms-plugin.structure-selection :: Structure -> Structure
*Create a molecular structure from the specified query expression.*
@@ -149,7 +177,7 @@
```
----------------------------
## <a name="ms-plugin-volume-from-ccp4"></a>ms-plugin.volume-from-ccp4 :: Ccp4 -> Data
-*Create Volume from CCP4/MRC data*
+*Create Volume from CCP4/MRC/MAP data*
### Parameters
- **voxelSize**: 3D vector [x, y, z]
@@ -294,7 +322,7 @@ Object with:
- **highlightColor**: Color as 0xrrggbb
- **selectColor**: Color as 0xrrggbb
- **quality**: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
- - **isoValue**: Numeric value
+ - **isoValueNorm**: Numeric value *(Normalized Isolevel Value)*
- **renderMode**: One of 'isosurface', 'volume'
- **controlPoints**: A list of 2d vectors [xi, yi][]
- **list**: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'
@@ -480,7 +508,7 @@ Object with:
- **highlightColor**: Color as 0xrrggbb
- **selectColor**: Color as 0xrrggbb
- **quality**: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
- - **isoValue**: Numeric value
+ - **isoValueNorm**: Numeric value *(Normalized Isolevel Value)*
- **renderMode**: One of 'isosurface', 'volume'
- **controlPoints**: A list of 2d vectors [xi, yi][]
- **list**: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'
--
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